Thursday, 2 December 2010

Arsenic Life - ZOMG! The straight dope on extremophiles and arsenic.

By now you may have heard today's big announcement in Science1 of the discovery of extremophile bacteria that use arsenic in their DNA rather than phosphorous. This discovery has been played up by the media (as usual) as being a major discovery that will cause scientists to "rewrite the story of life" or other such hyperbole-based headlines. And while definitely interesting, this discovery, unfortunately, is just not a major finding.

What the discovery is:

The team of researchers were concerned with a lake in California called Mono Lake. This lake itself is particularly interesting: it is highly alkaline, with a pH at around 10, so it is very basic (remember that water has a neutral pH of 7, and that the pH scale is logarithmic, so the lake is 1000 times more alkaline than a regular freshwater lake). The lake also contains quite high levels of arsenic, an element that is highly poisonous to life. The scientists, aware that extremophile bacteria just love to live in what we would normally consider absolutely hostile conditions, were curious about what kind of microbial life lived in the lake.

What they found were microbes that not only lived happily in the highly alkaline, arsenic-laden conditions, but actually utilized arsenic in place of phosphorous in their biochemistry: their DNA contained arsenic where it normally would have a phosphate backbone and even some of their amino acids contained arsenic instead of phosphorous. They did this by growing the bacteria in media containing radiolabelled arsenic, and after allowing the bacteria time to utilize the arsenic as they pleased, found that the radiolabelled atoms ended up in the DNA, amino acids and other normally phosphorus-containing molecules.

What this DOESN'T mean:

This does not mean we have discovered "alien" life, like some media outlets have been saying. Such life easily fits in with what we know about extremophile bacteria - they are resilient enough to find a way to use toxic environments to their advantage.

It also doesn't mean that we need to re-examine the way we think early life evolved. It is unlikely this discovery says anything about evolutionary history (though it might say volumes about how evolution can be incredibly innovative!).

What it DOES mean:

It does mean that evolution can work in wondrous ways that we hadn't even imagined. Make no mistake, however - this finding surely fits within current evolutionary theory.

It also means, on a more hypothetical level, that astrobiologists may need to broaden their definitions of "life" when searching for the signs of life outside of our planetary system.

Why this discovery isn't as big of a deal as it first seems:

Although at first the announcement of life that uses arsenic as a building block is exciting, a little critical thinking shows that there is reason for skepticism. The researchers studied the microbes by slowly increasing the level of arsenic in the media they were grown in. After multiple rounds of this, they were left with microbes that were found to have arsenic in their DNA and amino acids. However, this method leaves open the possibility that they were simply selecting for microbes that could use arsenic under high arsenic/low phosphorous levels. In other words, this experiment does not show that using arsenic is the natural way these microbes live. It is entirely possible that they use phosphorous for their important biochemical molecules like ever other microbe, and under stressful conditions, switch to different mode where they use arsenic instead. It's even possible that after successive rounds of increasing arsenic content, the team artificially selected for microbes that had this ability: in effect, they may have forced the microbes to evolve a new pathway that does not exist in nature.

This finding doesn't say alot about evolutionary history either: Lake Mono is a relativley recent geological feature, so it's likely the microbes adapted to such an environment relatively recently also.

Furthermore, the team did not attempt to determine HOW the bacteria incorporate arsenic into their DNA and amino acids: what biochemical pathways are involved? Do they use NTAs instead of NTPs? How stable would such molecules be - phosphate plays an important role in stabilizing the structure of DNA, so would the use of arsenic affect this? Are such molecules recognised by the microbes' DNA polymerase? Or by any important enzymes, for that matter? Arsenic is a larger atom than phosphorous - will this alter the shape and size of the major and minor grooves and if so, how does this affect the binding of proteins? Is arsenic ALWAYS used by these microbes, even in low arsenic/high phosphorous levels? These questions are just begging to be answered, and until they are, I think the vast majority of molecular biologists and biochemists will remain skeptical.

An interesting find, for sure - the very fact that organisms can use arsenic to live is exciting - but a "new form of life" or even "arsenic-based life"? Well, there's really no evidence to support such claims at the moment.

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PZ over at Pharyngula has a great rundown of why calling this "arsenic based life" is silly, echoing many of the points I made above.